Biochemistry Glossary

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A form. A duplex DNA structure with right-handed twisting in which the planes of the base pairs are tilted about 70 with respect to the helix axis.

Acetal. The product formed by the successive condensation of two alcohols with a single aldehyde. It contains two ether-linked oxygens attached to a central carbon atom.

Acetyl CoA. Acetyl-coenzyme A, a high-energy ester of acetic acid that is important both in the tricarboxylic acid cycle and in fatty acid biosynthesis.

Actin. A protein found in combination with myosin in muscle and also found as filaments constituting an important part of the cytoskeleton in many eukaryotic cells.

Actinomycin D. An antibiotic that binds to DNA and inhibits RNA chain elongation.

Activated complex. The highest free energy state of a complex in going from reactants to products.

Active site. The region of an enzyme molecule that contains the substrate binding site and the catalytic site for converting the substrate(s) into product(s).

Active transport. The energy-dependent transport of a substance across a membrane.

Adenine. A purine base found in DNA or RNA.

Adenosine. A purine nucleoside found in DNA, RNA, and many cofactors.

Adenosine diphosphate (ADP). The nucleotide formed by adding a pyrophosphate group to the 5'-OH group of adenosine.

Adenosine triphosphate (ATP). The nucleotide formed by adding yet another phosphate group to the pyrophosphate group on ADP.

Adenylate cyclase. The enzyme that catalyzes the formation of cyclic 3',5' adenosine monophosphate (cAMP) from ATP.

Adipocyte. A specialized cell that functions as a storage depot for lipid.

Aerobe. An organism that utilizes oxygen for growth.

Affinity chromatography. A column chromatographic technique that employs attached functional groups that have a specific affinity for sites on particular proteins.

Alcohol. A molecule with a hydroxyl group attached to a carbon atom.

Aldehyde. A molecule containing a doubly bonded oxygen and a hydrogen attached to the same carbon atom.

Alleles. Alternative forms of a gene.

Allosteric enzyme. An enzyme whose active site can be altered by the binding of a small molecule at a nonoverlapping site.

Angstrom (Å). A unit of length equal to 10-10 m.

Anomers. The sugar isomers that differ in configuration about the carbonyl carbon atom. This carbon atom is called the anomeric carbon atom of the sugar.

Antibiotic. A natural product that inhibits bacterial growth (is bacteriostatic) and sometimes results in bacterial death (is bacteriocidal).

Antibody. A specific protein that interacts with a foreign substance (antigen) in a specific way.

Anticodon. A sequence of three bases on the transfer RNA that pair with the bases in the corresponding codon on th messenger RNA.

Antigen. A foreign substance that triggers antibody formation and is bound by the corresponding antibody.

Antiparallel b-pleated sheet (b-sheet). A hydrogen bonded secondary structure formed between two or more extended polypeptide chains.

Apoactivator. A regulatory protein that stimulates transcription from one or more genes in the presence of a coactivator molecule.

Asexual reproduction. Growth and cell duplication that does not involve the union of nuclei from cells of opposite mating types.

Asymmetric carbon. A carbon that is covalently bonded to four different groups.

Attenuator. A provisional transcription stop signal.

Autoradiography. The technique of exposing film in the presence of disintegrating radioactive particles. Used to obtain information on the distribution of radioactivity in a gel or a thin cell section.

Autoregulation. The process in which a gene regulates its own expression.

Autotroph. An organism that can form its organic constituents from CO2.

Auxin. A plant growth hormone usually concentrated in the apical bud.

Auxotroph. A mutant that cannot grow on the minimal medium on which a wild-type member of the same species can grow.

Avogadro's number. The number of molecules in a gram molecular weight of any compound (6.023 x 1023).


B cell. One of the major types of cells in the immune system. B cells can differentiate to form memory cells or antibody-forming cells.

B form. The most common form of duplex DNA, containing a right-handed helix and about 10 (10.5 exactly) base pairs per turn of the helix axis.

Beta-bend (b-bend) or turn. A characteristic way of turning an extended polypeptide chain in a different direction, involving the minimum number of residues, and held together by hydrogen bonding.

Beta-sheet (b-sheet). A sheetlike structure formed by the interaction between two or more extended polypeptide chains.

Beta-oxidation (b-oxidation). Oxidative degradation of fatty acids that occurs by the successive oxidation of the b-carbon atom.

Base. The adenine, guanine, cytosine or thymine group attached to a nucleotide or nucleoside. Also may be used to refer to a nucleic acid unit within a polynucleotide chain, as when a gene is said to be 2000 bases long.

Base analog. A compound, usually a purine or a pyrimidine, that differs somewhat from a normal nucleic acid base.

Base stacking. The close packing of the planes of base pairs, commonly found in DNA and RNA structures.

Bidirectional replication. Replication in both directions away from the origin, as opposed to replication in one direction only (unidirectional replication).

Bilayer. A double layer of lipid molecules with the hydrophilic ends oriented outward, in contact with water, and the hydrophobic parts oriented inward.

Bile salts. Derivatives of cholesterol with detergent properties that aid in the solubilization of lipid molecules in the digestive tract.

Biochemical pathway. A series of enzyme-catalyzed reactions that results in the conversion of a precursor molecule into a product molecule.

Bioluminescence. The production of light by a biochemical system.

Blastoderm. The stage in embryogenesis when a unicellular layer at the surface surrounds the yolk mass.

Bond energy. The energy required to break a bond.

Branchpoint. An intermediate in a biochemical pathway that can follow more than one route in following steps.

Buffer. A conjugate acid-base pair that is capable of resisting changes in pH when acid or base is added to the system. This tendency will be maximal when the conjugate forms are present in equal amounts.


cAMP. 3',5' cyclic adenosine monophosphate. The cAMP molecule plays a key role in metabolic regulation.

CAP. The catabolite gene activator protein, sometimes incorrectly referred to as the CRP protein. The latter term, in small letters (crp), should be used to refer to the gene but not to the protein.

Capping. Covalent modification involving the addition of a modified guanidine group in a 5'-5" linkage. It occurs only in eukaryotes, primarily on mRNA molecules.

Carbohydrate. A polyhydroxy aldehyde or ketone.

Carboxylic acid. A molecule containing a carbon atom attached to a hydroxyl group and to an oxygen atom by a double bond.

Carcinogen. A chemical that can cause cancer.

Carotenoids. Lipid-soluble pigments that are made from isoprene units.

Catabolism. That part of metabolism that is concerned with degradation reactions.

Catabolite repression. The general repression of transcription of genes associated with catabolism that is seen in the presence of glucose.

Catalyst. A compound that lowers the activation energy of a reaction without itself being consumed.

Catalytic site. The site of an enzyme involved in the catalytic process.

Catenane. An interlocked pair of circular structures, such as covalently closed DNA molecules.

Catenation. The linking of molecules without any direct covalent bonding between them, as when two circular DNA molecules interlock like the links in a chain.

cDNA. Complementary DNA, made in vitro from the mRNA by the enzyme reverse transcriptase using deoxyribonucleotide triphosphates. Unlike mRNA, cDNA can be easily propagated and sequenced.

Cell commitment. That stage in a cell's life when it be comes committed to a certain line of development.

Cell cycle. All of those stages that a cell passes through from one cell generation to the next.

Cell line. An established clone originally derived from a whole organism through a long process of cultivation.

Cell lineage. The pedigree of cells resulting from binary fission.

Cell wall. A tough outer coating found in many plant, fungal, and bacterial cells that accounts for their ability to withstand mechanical stress or abrupt changes in osmotic pressure. Cell walls always contain a carbohydrate component and frequently also a peptide and a lipid component.

Chelate. A molecule that contains more than one binding site and frequently binds to another molecule through more than one binding site at the same time.

Chemiosmotic coupling. The coupling of ATP synthesis to an electrochemical potential gradient across a membrane.

Chimeric DNA. Recombinant DNA whose components originate from two or more different sources.

Chiral compound. A compound that can exist in two forms that are non-superimposable images of one another.

Chlorophyll. A green photosynthetic pigment that is made of a magnesium dihydroporphyrin complex.

Chloroplast. A chlorophyll-containing photosynthetic organelle, found in eukaryotic cells, that can harness light energy.

Chromatin. The nucleoprotein fibers of eukaryotic chromosomes.

Chromatography. A procedure for separating chemically similar molecules. Segregation is usually carried out on paper or in glass or metal columns with the help of different solvents. The paper or glass columns contain porous solids with functional groups that have limited affinities for the molecules being separated.

Chromosome. A thread-like structure, visible in the cell nucleus during metaphase, that carries the hereditary information.

Chromosome puff. A swollen region of a giant chromosome; the swelling reflects a high degree of transcription activity.

Cis dominance. Property of a sequence or a gene that exerts a dominant effect on a gene to which it is linked.

Cistron. A genetic unit that encodes a single polypeptide chain.

Citric acid cycle. See tricarboxylic acid (TCA) cycle.

Clone. One of a group of genetically identical cells or organisms derived from a common ancestor.

Cloning vector. A self-replicating entity to which foreign DNA can be covalently attached for purposes of amplification in host cells.

Coactivator. A molecule that functions together with a protein apoactivator. For example, cAMP is a coactivator of the CAP protein.

Codon. In a messenger RNA molecule, a sequence of three bases that represents a particular amino acid.

Coenzyme. An organic molecule that associates with enzymes and affects their activity.

Cofactor. A small molecule required for enzyme activity. It could be organic in nature, like a coenzyme, or inorganic in nature, like a metallic cation.

Complementary base sequence. For a given sequence of nucleic acids, the nucleic acids that are related to them by the rules of base pairing.

Configuration. The spatial arrangement in which atoms are covalently linked in a molecule.

Conformation. The three-dimensional arrangement adopted by a molecule, usually a complex macromolecule. Molecules with the same configuration can have more than one conformation.

Consensus sequence. In nucleic acids, the "average" sequence that signals a certain type of action by a specific protein. The sequences actually observed usually vary around this average.

Constitutive enzymes. Enzymes synthesized in fixed amounts, regardless of growth conditions.

Cooperative binding. A situation in which the binding of one ligand to a macromolecule favors the binding of another. For example, DNA cooperatively binds histone molecules, and hemoglobin cooperatively binds oxygen molecules.

Coordinate induction. The simultaneous expression of two or more genes.

Cosmid. A DNA molecule with cos ends from lambda-bacteriophage that can be packaged in vitro into a virus for infection purposes .

Cot curve. A curve that indicates the rate of DNA-DNA annealing as a function of DNA concentration and time.

Cytidine. A pyrimidine nucleoside found in DNA and RNA.

Cytochromes. Heme-containing proteins that function as electron carriers in oxidative phosphorylation and photosynthesis.

Cytokinin. A plant hormone produced in root tissue.

Cytoplasm. The contents enclosed by the plasma (or cytoplasmic) membrane, excluding the nucleus.

Cytosine. A pyrimidine base found in DNA and RNA.

Cytoskeleton. The filamentous skeleton, formed in the eukaryotic cytoplasm, that is largely responsible for controlling cell shape.

Cytosol. The liquid portion of the cytoplasm, including the macromolecules but not including the larger structures like subcellular organelles or cytoskeleton.


D loop. An extended loop of single-stranded DNA displaced from a duplex structure by an oligonucleotide.

Dalton. A unit of mass equivalent to the mass of a hydrogen atom (1.66 x 10-24 g)

Dark reactions. Reactions that can occur in the dark, in a process that is usually associated with light, such as the dark reactions of photosynthesis.

De novo pathway. A biochemical pathway that starts from elementary substrates and ends in the synthesis of a biochemical.

Deamination. The enzymatic removal of an amine group, as in the deamination of an amino acid to an alpha keto acid.

Dehydrogenase. An enzyme that catalyzes the removal of a pair of electrons (and usually one or two protons) from a substrate molecule.

Denaturation. The disruption of the native folded structure of a nucleic acid or protein molecule; may be due to heat, chemical treatment, or change in pH.

Density-gradient centrifugation. The separation, by centrifugation, of molecules according to their density, in a gradient varying in solute concentration.

Dialysis. Removal of small molecules from a macromolecule preparation by allowing them to pass across a semipermeable membrane.

Diauxic growth. Biphasic growth on a mixture of two carbon sources in which one carbon source is used up before the other one. For example, in the presence of glucose and lactose, E. coli will utilize the glucose before the lactose.

Difference spectra. Plots comparing the absorption spectra of a molecule or an assembly of molecules in different states, for example, those of mitochondria under oxidizing or reducing conditions.

Differential centrifugation. Separation of molecules and/or organelles by sedimentation rate.

Differentiation. A change in the form and pattern of a cell and the genes it expresses as a result of growth and replication, usually during development of a multicellular organism. Also occurs in microorganisms (e.g. in sporulation).

Dimer. Structure resulting from the association of two subunits.

Diploid cell. A cell that contains two chromosomes (2N) of each type.

Dipole. A separation of charge within a single molecule.

Directed mutagenesis. In a DNA sequence, an intentional alteration that can be genetically inherited.

Dissociation constant. An equilibrium constant for the dissociation of a molecule into two parts (e.g., dissociation of acetic acid into acetate anion and a proton); Kd.

Disulfide bridge. A covalent linkage formed by oxidation between two cysteine SH groups either in the same polypeptide chain or in different polypeptide chains. Reversible by adding reducing agents.

DNA. Deoxyribonucleic acid. A polydeoxyribonucleotide in which the sugar is deoxyribose; the main repository of genetic information in all cells and most viruses.

DNA cloning. The propagation of individual segments of DNA as clones.

DNA library. A mixture of clones, each containing a cloning vector and a segment of DNA from a source of interest.

DNA polymerase. An enzyme that catalyzes the formation of 3'-5' phosphodiester bonds from deoxyribonucleotide triphosphates.

Domain. A segment of a folded protein structure showing conformational integrity. A domain could include the entire protein or just a fraction of the protein. Some proteins, such as antibodies, contain many structural domains.

Dominant. Describing an allele whose phenotype is expressed regardless of whether the organism is homozygous or heterozygous for that allele.

Double helix. A structure in which two helically-twisted polynucleotide strands are held together by hydrogen bonding and base stacking.

Duplex. Same as double helix.

Dyad symmetry. Property of a structure that can be rotated by 180 to produce the same structure.


Ecdysone. A hormone that stimulates the molting process in insects.

Edman degradation. A systematic method of sequencing proteins, proceeding by stepwise removal of single amino acids from the amino terminus of a polypeptide chain.

Eicosanoid. Any fatty acid with 20 carbons.

Electrophoresis. The movement of particles in an electrical field. A commonly-used technique for analysis of mixtures of molecules in solution according to their electrophoretic mobilities.

Elongation factors. Protein factors uniquely required during the elongation phase of protein synthesis. Elongation factor G (EF-G) brings about the movement of the peptidyl tRNA from the A site to the P site of the ribosome.

Eluate. The fluid that has passed through (eluted from) a chromatographic column.

Embryo. Plant or animal at an early stage of development.

Enantiomorphs. Isomers that are mirror images of one another.

Endergonic reaction. A reaction with a positive standard free energy change.

End-product (feedback) inhibition. The inhibition of the first enzyme in a pathway by the end product of that pathway.

Endocrine glands. Specialized tissues whose function is to synthesize and secrete hormones.

Endonuclease. An enzyme that breaks a phosphodiester linkage at some point within a polynucleotide chain.

Endopeptidase. An enzyme that breaks a polypeptide chain at an internal peptide linkage.

Endoplasmic reticulum. A system of double membranes in the cytoplasm that is involved in the synthesis of transported proteins. The rough endoplasmic reticulum has ribosomes associated with it. The smooth endoplasmic reticulum does not.

Energy charge. The fractional degree to which the AMP-ADP-ATP system is filled with high-energy phosphates (phosphoryl groups).

Enhancer. A DNA sequence that can stimulate transcription at an appreciable distance from the site where it is located. It acts in either orientation and either upstream or downstream from the promoter.

Entropy. The randomness of a system.

Enzyme. A moleucle, most often a protein, that contains a catalytic site for a biochemical reaction.

Epimers. Two stereoisomers with more than one chiral center that differ in configuration at one of their chiral centers.

Equilibrium. The point at which the concentrations of two compounds are such that the interconversion of one compound into the other compound does not result in any change in free energy.

Escherichia coli (E. coli). A Gram negative bacterium commonly found in the vertebrate intestine. It is the bacterium most frequently used in the study of biochemistry and genetics.

Established cell line. A group of cultured cells derived from a single origin and capable of stable growth for many generations.

Ether. A molecule containing two carbons linked by an oxygen atom.

Eukaryote. A cell or organism that has a membrane-bound nucleus.

Excision repair. DNA repair in which a damaged region is replaced.

Excited state. An energy-rich state of an atom or a molecule, produced by the absorption of radiant energy.

Exergonic reaction. A chemical reaction that takes place with a negative change in standard free energy.

Exon. A segment within a gene that carries part of the coding information for a protein.

Exonuclease. An enzyme that breaks a phosphodiester linkage at one or the other end of a polynucleotide chain so as to release single or small nucleotide residues.


F factor. A large bacterial plasmid, known as the sex-factor plasmid because it permits mating between F+ and F- bacteria.

Facultative aerobe. An organism that can use molecular oxygen in its metabolism but that also can live anaerobically.

Fatty acid. A long-chain hydrocarbon containing a carboxyl group at one end. Saturated fatty acids have completely saturated hydrocarbon chains. Unsaturated fatty acids have one or more carbon-carbon double bonds in their hydrocarbon chains.

Feedback inhibition. See end-product inhibition.

Fermentation. The energy-generating breakdown of glucose or related molecules by a process that does not require molecular oxygen.

Fingerprinting. The characteristic two-dimensional paper chromatogram obtained from the partial hydrolysis of a protein or a nucleic acid.

Fluorescence. The emission of light by an excited molecule in the process of making the transition from the excited state to the ground state.

Frameshift mutations. Insertions or deletions of genetic material that lead to a shift in the translation of the reading frame. The mutation usually leads to nonfunctional proteins.

Free energy. That part of the energy of a system that is available to do useful work.

Furanose. A sugar that contains a five-membered ring as a result of intramolecular hemiacetal formation.

Futile cycle. See pseudocycle.


G1 phase. That period of the cell cycle in which preparations are being made for chromosome duplication, which takes place in the S phase.

G2 phase. That period of the cell cycle between S phase and mitosis (M phase).

Gametes. The ova and the sperm, haploid cells that unite during fertilization to generate a diploid zygote.

Gel fitration chromatography. A technique that makes use of certain polymers that can form porous beads with varying pore sizes. In columns made from such beads, it is possible to separate molecules, which cannot penetrate beads of a given pore size, from small molecules that can. Also called gel-exclusion or molecular seive chromatography.

Gene. A segment of the genome that codes for a functional product.

Gene amplification. The duplication of a particular gene within a chromosome two or more times.

Gene splicing. The cutting and rejoining of DNA sequences.

General recombination. Recombination that occurs between homologous chromosomes at homologous sites.

Generation time. The time it takes for a cell to double its mass under specified conditions.

Genetic map. The arrangement of genes or other identifiable sequences on a chromosome.

Genome. The total genetic content of a cell or a virus.

Genotype. The genetic characteristics of an organism (distinguished from its observable characteristics, or phenotype).

Globular protein. A folded protein that adopts an approximately globular shape. May also be called soluble proteins.

Gluconeogenesis. The production of sugars from nonsugar precursors such as lactate or amino acids. Applies more specifically to the production of free glucose by vertebrate livers.

Glycogen. A polymer of glucose residues in 1,4 linkage, with 1,6 linkages at branchpoints.

Glycogenic. Describing amino acids whose metabolism may lead to gluconeogenesis.

Glycolipid. A lipid containing a carbohydrate group.

Glycolysis. The catabolic conversion of glucose to pyruvate with the production of ATP.

Glycoprotein. A protein linked to an oligosaccharide or a polysaccharide. Glycosaminoglycans. Long, unbranched polysaccharide chains composed of repeating disaccharide subunits in which one of the two sugars is either N-acetylglucosamine or N-acetylgalactosamine.

Glycosidic bond. The bond between a sugar and an alcohol. Also the bond that links two sugars in disaccharides, oligosaccharides, and polysaccharides.

Glyoxylate cycle. A pathway that uses some of the enzymes of the TCA cycle and some enzymes whereby acetate can be converted into succinate and carbohydrates.

Glyoxysome. An organelle containing some enzymes of the glyoxylate cycle.

Goldman equation. An equation expressing the quantitative relationship between the concentrations of charged species on either side of a membrane and the resting transmembrane potential.

Golgi apparatus. A complex series of double-membrane structures that interact with the endoplasmic reticulum and that serve as a transfer point for proteins destined for other organelles, the plasma membrane, or extracellular transport.

Gram molecular weight. For a given compound, the weight in grams that is numerically equal to its molecular weight.

Ground state. The lowest electronic energy state of an atom or a molecule.

Growth factor. A substance that must be present in the growth medium to permit eucaryotic cell proliferation.

Growth fork. The region on a DNA duplex molecule where synthesis is taking place. It resembles a fork in shape, since it consists of a region of duplex DNA connected to a region of unwound single strands.

Guanine. A purine base found in DNA or RNA.

Guanosine. A purine nucleoside found in DNA and RNA.


Hairpin loop. A single-stranded complementary region of DNA or RNA that folds back on itself and base-pairs into a double helix.

Half-life. The time required for the disappearance of one half of a substance.

Haploid cell. A cell containing only one chromosome of each type.

Heavy isotopes. Forms of atoms that contain greater numbers of neutrons than the most common form (e.g., 15N, l3C).

Helix. A spiral structure with a repeating pattern.

Heme. An iron-porphyrin complex found in hemoglobin and cytochromes. Hemiacetal. The product formed by the condensation of an aldehyde with an alcohol; it contains one oxygen linked to a central carbon in a hydroxyl fashion and one oxygen linked to the same central carbon by an ether linkage.

Henderson-Hasselbalch equation. An equation that relates the pKa, to the pH and the ratio of the proton acceptor (A-) and the proton donor (HA) species of a conjugate acid base pair.

Heterochromatin. Highly condensed regions of chromosomes that are not usually transcriptionally active.

Heteroduplex. An annealed duplex structure between two DNA strands that do not show perfect complementarity. Can arise by mutation, recombination, or the annealing of complementary single-stranded DNAs.

Heteropolymer. A polymer containing more than one type of monomeric unit.

Heterotroph. An organism that requires preformed organic compounds for growth.

Heterozygous. Describing an organism (a heterozygote) that carries two different alleles for a given gene.

Hexose. A sugar with a six-carbon backbone.

High-energy compound. A compound that undergoes hydrolysis with a high negative standard free energy change.

Histones. The family of basic proteins that is normally associated with DNA in most cells of eukaryotic organisms.

Holoenzyme. An intact enzyme containing all of its subunits and any necessary cofactors with full enzymatic activity.

Homologous chromosomes. Chromosomes that carry the same pattern of genes, but not necessarily the same alleles.

Homopolymer. A polymer composed of only one type of monomeric building block.

Homozygous. Describing an organism (a homozygote) that carries two identical alleles for a given gene.

Hormone. A chemical substance made in one cell and secreted so as to influence the metabolic activity of a select group of cells located at other sites in the organism.

Hormone receptor. A protein that is located on the cell membrane or inside the responsive cell and that interacts specifically with the hormone.

Host cell. A cell used for growth and reproduction of a virus.

Hybrid (or chimeric) plasmid. A plasmid that contains DNA from two different organisms.

Hydrogen bond. A weak, noncovalent, attractive force between one electronegative atom and a hydrogen atom that is covalently linked to a second electronegative atom.

Hydrolysis. The cleavage of a molecule by the addition of water. Hydrophilic. Preferring to be in contact with water.

Hydrophobic. Preferring not to be in contact with water, as is the case with the hydrocarbon portion of a fatty acid or phospholipid chain.

Hydrophobic effect. The noncovalent association of nonpolar groups with each other in aqueous solution.

Hydroxyapatite. A calcium phosphate gel used, in the case of nucleic acids, to selectively absorb duplex DNA-RNA from a mixture of single-stranded and duplex nucleic acids.


Icosahedral symmetry. The symmetry displayed by a regular polyhedron that is composed of 20 equilateral triangular faces with 12 corners.

Imine. A molecule containing a nitrogen atom attached to a carbon atom by a double bond. The nitrogen is also covalently linked to a hydrogen. Immunofluorescence. A cytological technique in which a specific fluorescent antibody is used to label an antigen. Frequently used to determine the location of an antigen in a tissue or a cell.

Immunoglobulin. A protein made in a B plasma cell and usually secreted; it interacts specifically with a foreign agent. Synonymous with antibody. It is composed of two heavy and two light chains linked by disulfide bonds. Immunoglobulins can be divided into five classes (IgG, IgM, IgA, IgD, and IgE) based on their heavy-chain component.

Inducible proteins. Those which are synthesized in different amounts depending on cellular signals.

In vitro. Literally, "in glass," describing whatever happens in a test tube or other receptacle, as opposed to what happens in whole cells of the whole organism (in vivo).

Induced fit. A change in the shape of an enzyme that results from the binding of substrate.

Inducers. Molecules that cause an increase in a protein activity when added to cells.

Initiation factors. Those protein factors that are specifically required during the initiation phase of protein synthesis.

Intercalating agent. A chemical, usually containing aromatic rings, that can sandwich in-between adjacent base pairs in a DNA duplex. The intercalation leads to an adjustment in the DNA secondary structure, as adjacent base pairs are usually close-packed.

Interferon. One of a family of proteins that are liberated by special host cells in the mammal in response to viral infection. The interferons attach to an infected cell, where they stimulate antiviral protein synthesis.

Intervening sequence. See intron.

Intron. A segment of the nascent transcript that is removed by splicing. Also refers to the corresponding region in the DNA. Synonymous with intervening sequence.

Inverted repeat. A chromosome segment that is identical to another segment on the same chromosome except that it is oriented in the opposite direction.

Ion-exchange resin. A polymeric resinous substance, usually in bead form, that contains fixed groups with positive or negative charge. An anion exchange resin has positively-charged groups and is therefore useful in exchanging the anionic groups in a test sample; a cation exchange resin is itself negatively charged, and has the opposite application. The resin is usually used in a column chromatographic procedure.

Isoelectric point or pH. The pH at which a protein has no net charge.

Isomerase. An enzyme that catalyzes an intramolecular rearrangement.

Isomerization. Rearrangement of atomic groups within the same molecule without any loss or gain of atoms.

Isozymes. Multiple forms of an enzyme that differ from one another in one or more of the properties.


Km. See Michaelis constant.

Ketogenic. Describing amino acids that are metabolized to acetoacetate and acetate.

Ketone. A functional group of an organic compound in which a carbon atom is double-bonded to an oxygen. Neither of the other substituents attached to the carbon is a hydrogen. Otherwise the group would be called an aldehyde.

Ketone bodies. Refers to acetoacetate, acetone, and b-hydroxybutyrate made from acetyl-CoA in the liver and used for energy in nonhepatic tissue.

Ketosis. A condition in which the concentration of ketone bodies in the blood or urine is unusually high.

Kilobase. One thousand bases in a DNA molecule.

Kinase. An enzyme catalyzing phosphorylation of an acceptor molecule, usually with ATP serving as the phosphate (phosphoryl) donor.

Kinetochore. A structure that attaches laterally to the centromere of a chromosome; it is the site of chromosome tubule attachment.

Krebs cycle. See tricarboxylic acid (TCA) cycle.


Lampbrush chromosome. Giant diplotene chromosome found in the oocyte nucleus. The loops that are observed are the sites of extensive gene expression.

Law of mass action. The finding that the rate of a chemical reaction is a function of the product of the concentrations of the reacting species.

Leader region. The region of an mRNA between the 5' end and the initiation codon for translation of the first polypeptide chain.

Leader sequence. An N-terminal signal sequence that directs secretion and processing of proteins.

Lectins. Agglutinating proteins usually extracted from plants.

Ligand. A (usually small) molecule that binds to another, such as oxygen when it binds to myoglobin.

Ligase. An enzyme that catalyzes the joining of two molecules together. In DNA it joins 5'-OH to 3' phosphates.

Linkage. The tendency of markers to be inherited together. Linkage of two markers is an indication that they are close to one another in the genome.

Linkers. Short oligonucleotides that can be ligated (connected) to larger DNA fragments, then cleaved (cut) to yield overlapping cohesive (sticky) ends, suitable for ligation to other DNAs that contain comparable cohesive ends.

Linking number. The net number of times one polynucleotide chain crosses over another polynucleotide chain. By convention, right-handed crossovers are given a plus designation.

Lipid. A biological molecule that is soluble in organic solvents. Lipids include steroids, fatty acids, prostaglandins, terpenes, and waxes.

Lipid bilayer. Model for the structure of the cell membrane based on the interaction between the hydrophobic regions of phospholipids.

Lipopolysaccharide. Usually refers to a unique glycolipid found in Gram negative bacteria.

Lyase. An enzyme that catalyzes the removal of a group to form a double bond, or the reverse reaction.

Lysogenic virus. A virus that can adopt an inactive (Iysogenic) state, in which it maintains its genome within a cell instead of entering the Iytic cycle. The circumstances that determine whether a Iysogenic (temperate) virus will adopt an inactive state or an active Iytic state are often subtle and depend upon the physiologic state of the infected cell.

Lysosome. An organelle that contains hydrolytic enzymes designed to break down proteins that are targeted to that organelle.

Lytic infection. A virus infection that leads to the Iysis of the host cell, yielding progeny virus particles.


M phase. That period of the cell cycle when mitosis takes place.

Marker. A "landmark" that can be localized to a specific region of the genome.

Meiosis. Process in which diploid cells undergo division to form haploid sex cells.

Membrane. A sheet-like composite of protein and lipid that is the boundary of cells and organelles.

Membrane protein. A protein that is associated with a membrane, rather than found free in the cell. A membrane protein may be integral (embedded or buried) in the membrane, or peripheral (attached more loosely, by interactions with either lipid or intergral membrane proteins).

Membrane transport. The facilitated transport of a molecule across a membrane.

Merodiploid. An organism that is diploid for some but not all of its genes.

Mesosome. An invagination of the bacterial cell membrane.

Messenger RNA (mRNA). The template RNA carrying the message for protein synthesis.

Metabolic turnover. A measure of the rate at which already existing molecules of the given species are replaced by newly-synthesized molecules of the same type. Usually isotopic labeling is required to measure turnover.

Metabolism. The sum total of the enzyme-catalyzed reactions that occur in a living organism.

Metamorphosis. A change of form, especially the conversion of a larval form to an adult form.

Metaphase. That stage in mitosis or meiosis when all of the chromosomes are lined up on the equator (i.e., an imaginary line that bisects the cell).

Micelle. An aggregate of lipids in which the polar head groups face outward and the hydrophobic tails face inward; no solvent is trapped in the center.

Michaelis constant (Km). The substrate concentration at which an enzyme-catalyzed reaction proceeds at one-half of the maximum velocity.

Michaelis-Menten equation (also known as the Henri-Michaelis-Menten equation). An equation relating the reaction velocity to the substrate concentration of an enzyme.

Microtubules. Thin tubules, made from globular proteins, that serve multiple purposes in eukaryotic cells.

Mismatch repair. The replacement of a base in a heteroduplex structure by one that forms a Watson-Crick base pair.

Missense mutation. A change in which a codon for one amino acid is replaced by a codon for another amino acid.

Mitochondrion. An organelle, found in eukaryotic cells, in which oxidative phosphorylation takes place. It contains its own genome and unique ribosomes to carry out protein syn thesis of only a fraction of the proteins located in this organelle.

Mitosis. The process whereby replicated chromosomes segregate equally toward opposite poles prior to cell division.

Mobile genetic element. A segment of the genome that can move as a unit from one location on the genome to another, without any requirement for sequence homology.

Molecular seive chromatography. See Gel filtration chromatography.

Molecular weight. See Gram molecular weight.

Molecularity of a reaction. The number of molecules involved in a specific reaction step.

Monolayer. A single layer of oriented lipid molecules.

Monomer. One unit of a protein or other structure.

Mutagen. An agent that can bring about a heritable change (mutation) in an organism.

Mutagenesis. A process that leads to a change in the genetic material that is inherited in later generations.

Mutant. An organism that carries an altered gene or change in its genome.

Mutarotation. The change in optical rotation of a sugar that is observed immediately after it is dissolved in aqueous solution, as the result of the slow approach of equilibrium of a pyranose or a furanose in its alpha and beta forms.

Mutation. The genetically inheritable alteration of a gene or group of genes.

Myofibril. A unit of thick and thin filaments in a muscle fiber.

Myosin. The main protein of the thick filaments in a muscle myofibril. It is composed of two coiled subunits (Mr about 220,000) that can aggregate to form a thick filament, which is globular at each end.


Nascent RNA. The initial transcripts of RNA, before any modification or processing.

Negative control. Repression of biological activity by the presence of a specific molecule.

Nernst equation. An equation that relates the redox potential to the standard redox potential and the concentrations of the oxidized and reduced form of the couple.

Nitrogen cycle. The passage of nitrogen through various valence states, as the result of reactions carried out by a wide variety of different organisms.

Nitrogen fixation. Conversion of atmospheric nitrogen into a form that can be converted by biochemical reactions to an organic form. This reaction is carried out by a very limited number of microorganisms.

Nitrogenous base. An aromatic nitrogen-containing molecule with basic properties. Such bases include purines and pyrimidines.

Noncompetitive inhibitor. An inhibitor of enzyme activity whose effect is not reversed by increasing the concentration of substrate molecule.

Nonsense mutation. A change in the base sequence that converts a sense codon (one that specifies an amino acid) to one that specifies a stop (a nonsense codon). There are three nonsense codons: amber, ochre and something I forget (let me know if you read this - S. Mowbray).

Northern blotting. See Southern blotting.

Nuclease. An enzyme that cleaves phosphodiester bonds of nucleic acids.

Nucleic acids. Polymers of the ribonucleotides or deoxyribonucleotides.

Nucleohistone. A complex of DNA and histone.

Nucleolus. A spherical structure visible in the nucleus during interphase. The nucleolus is associated with a site on the chromosome that is involved in ribosomal RNA synthesis.

Nucleophilic group. An electron-rich group that tends to attack an electron-deficient nucleus.

Nucleosome. A complex of DNA and an octamer of histone proteins in which a small stretch of the duplex is wrapped around a molecular bead of histone.

Nucleoside. An organic molecule containing a purine or pyrimidine base and a five-carbon sugar (ribose or deoxyribose).

Nucleotide. An organic molecule containing a purine or pyrimidine base, a five-carbon sugar (ribose or deoxyribose), and one or more phosphate groups. A phosphoester of a nucleoside.

Nucleus. In eukaryotic cells, the centrally-located organelle that encloses most of the chromosomes. Minor amounts of chromosomal substance are found in some other organelles, most notably the mitochondria and the chloroplasts.


Okazaki fragment. A short segment of single-stranded DNA that is an intermediate in DNA synthesis. In bacteria, Okazaki fragments are 1000-2000 bases in length; in eukaryotes, 100-200 bases in length.

Oligonucleotide. A polynucleotide containing a small number of nucleotides. The linkages are the same as in a polynucleotide; the only distinguishing feature is the small size.

Oligosaccharide. A molecule containing a small number of sugar residues joined in a linear or a branched structure by glycosidic bonds.

Oncogene. A gene of cellular or viral origin that is responsible for rapid, unruly growth of animal cells. A cancer-causing gene.

Operon. A group of contiguous genes that are coordinately regulated by two cis-acting elements, a promoter and an operator. Found only in prokaryotic cells.

Optical activity. The property of a molecule that leads to rotation of the plane of polarization of plane-polarized light when the latter is transmitted through the substance. Chirality is a necessary and sufficient property for optical activity.

Organelle. A subcellular membrane-bounded body with a well-defined function.

Osmotic pressure. The pressure generated by the mass flow of water to that side of a membrane-bounded structure that contains the higher concentration of solute molecules. A stable osmotic pressure is seen in systems in which the membrane is not permeable to some of the solute molecules.

Oxidation. The loss of electrons from a compound.

Oxidative phosphorylation. The formation of ATP as the result of the transfer of electrons to oxygen.

Oxido-reductase. An enzyme that catalyzes oxidation-reduction reactions.


Palindrome. A sequence of bases that reads the same in both directions on opposite strands of the DNA duplex (e.g., GAATTC).

PCR. Polymerase chain reaction. A method for amplifying DNA sequences.

Pentose. A sugar with five carbon atoms.

Pentose phosphate pathway. The pathway involving the oxidation of glucose-6-phosphate to pentose phosphates and further reactions of pentose phosphates.

Peptide. An organic molecule in which a covalent amide bond is formed between the a-amino group of one amino acid and the a-carboxyl group of another amino acid, with the elimination of a water molecule. The resulting connection is called a peptide bond.

Peptide mapping. Same as fingerprinting.

Peptidoglycan. The main component of the bacterial cell wall, consisting of a two-dimensional network of heteropolysaccharides running in one direction, cross-linked with polypeptides running in the perpendicular direction.

Periplasm. The region between the inner (cytoplasmic) membrane and the cell wall or outer membrane of a bacterium.

Permeable. The property of allowing material to pass through, as a permeable membrane.

Permease. A protein that catalyzes the transport of a specific small molecule across a membrane.

Peroxisomes. Subcellular organelles that contain flavin-requiring oxidases and that regenerate oxidized flavin by reaction with oxygen.

Phenotype. The observable trait(s) that result from the genotype in cooperation with the environment.

Phenylketonuria. A human disease caused by a genetic deficiency in the enzyme that converts phenylalanine to tyrosine. The immediate cause of the disease is an excess of phenylalanine, which can be alleviated by a diet low in phenylalanine.

Pheromone. A hormone-like substance that acts as an attractant.

Phosphodiester. A molecule containing two alcohols esterified to a single molecule of phosphate. For example, the backbone of nucleic acids is connected by 5'-3' phosphodiester linkages between the adjacent individual nucleotide residues.

Phosphogluconate pathway. Another name for the pentose phosphate pathway. This name derives from the fact that 6-phosphogluconate is an intermediate in the formation of pentoses from glucose.

Phospholipid. A lipid containing charged hydrophilic phosphate groups; a component of cell membranes.

Phosphorylation. The formation of a phosphate derivative of a biomolecule.

Photoreactivation. DNA repair in which the damaged region is repaired with the help of light and an enzyme. The lesion (break) is repaired without excision (cutting out) from the DNA.

Photosynthesis. The biosynthesis that directly harnesses the chemical energy resulting from the absorption of light. Frequently used to refer to the formation of carbohydrates from CO2 that occurs in the chloroplasts of plants or the plastids of photosynthetic microorganisms.

Pitch length (or pitch). The number of base pairs per turn of a duplex helix.

Plaque. A circular clearing on a lawn (continuous layer) of bacterial or culture cells, resulting from cell Iysis and production of phage or animal virus progeny.

Plasma membrane. The membrane that surrounds the cytoplasm.

Plasmid. A circular DNA duplex that replicates autonomously in bacteria. Plasmids that integrate into the host genome are called episomes. Plasmids differ from viruses in that they never form infectious nucleoprotein particles.

Polar group. A hydrophilic (water-loving) group.

Polar mutation. A mutation in one gene that reduces the expression of a gene or genes distal to the promoter in the same operon.

Polarimeter. An instrument for determining the rotation of polarization of light as the light passes through a solution containing an optically-active substance.

Polyamine. A hydrocarbon containing more than two amino groups.

Polycistronic messenger RNA. In prokaryotes, an RNA that contains two or more cistrons; note that only in prokaryotic mRNAs can more than one cistron be utilized by the translation system to generate individual proteins.

Polymerase. An enzyme that catalyzes the synthesis of a polymer from monomers.

Polynucleotide. A chain structure containing nucleotides linked together by phosphodiester (5'-3') bonds. The polynucleotide chain has a directional sense with a 5' and a 3' end.

Polynucleotide phosphorylase. An enzyme that polymerizes ribonucleotide diphosphates. No template is required.

Polypeptide. A linear polymer of amino acids held together by peptide linkages. The polypeptide has a directional sense, with an amino- and a carboxy-terminal end.

Polyribosome (polysome). A complex of an mRNA and two or more ribosomes actively engaged in protein synthesis.

Polysaccharide. A linear or branched chain structure containing many sugar molecules linked by glycosidic bonds.

Porphyrin. A complex planar structure containing four substituted pyrroles covalently joined in a ring and frequently containing a central metal atom. For example, heme is a porphyrin with a central iron atom.

Positive control. A system that is turned on by the presence of a regulatory protein.

Posttranslational modification. The covalent bond changes that occur in a polypeptide chain after it leaves the ribosome and before it becomes a mature protein.

Primary structure. In a polymer, the sequence of monomers and the covalent bonds. In proteins, it refers to the amino acid sequence.

Primer. A structure that serves as a growing point for polymerization. Short primers of DNA are often used in sequencing and mutagenesis procedures.

Primosome. A multiprotein complex that catalyzes synthesis of RNA primer at various points along the DNA template.

Prochiral molecule. A nonchiral molecule that lacks handedness and is optically inactive, but would become chiral by a change in one of the substituents at the chiral center. A prochiral molecule may react with an enzyme so that two groups that have a mirror-image relationship to each other are treated differently.

Prokaryote. A unicellular organism that contains a single chromosome, no nucleus, no membrane-bound organelles, and has characteristic ribosomes and biochemistry.

Promoter. That region of the gene that signals RNA polymerase binding and the initiation of transcription.

Prophage. The silent phage genome. Some prophages integrate into the host genome; others replicate autonomously. The prophage state is maintained by a phage-encoded repressor.

Prophase. The stage in meiosis or mitosis when chromosomes condense and become visible as refractile bodies.

Proprotein. A protein that is made in an active form, so that it requires processing to become functional.

Prostaglandin. An oxygenated eicosanoid that has a hormonal function. Prostaglandins are unusual hormones in that they usually have effects only in that region of the organism where they are synthesized.

Prosthetic group. Synonymous with coenzyme except that a prosthetic group is usually more firmly attached to the enzyme it serves.

Protamines. Highly basic, arginine-rich proteins found complexed to DNA in the sperm of many invertebrates and fish.

Protein subunit. One of the components or monomers of a multicomponent protein.

Proteoglycan. A protein-linked heteropolysaccharide in which the heteropolysaccharide is usually the major component.

Protist. A relatively undifferentiated organism that can survive as a single cell.

Proton acceptor. A functional group capable of accepting a proton from a proton donor molecule.

Proton motive force (Dp). The thermodynamic driving force for proton translocation.

Proto-oncogene. A cellular gene that can undergo modification to a cancer-causing gene (oncogene).

Pseudocycle. A sequence of reactions that can be arranged in a cycle but that usually do not function simultaneously in both directions. Also called a futile cycle, since the net result of simultaneous functioning in both directions would be the expenditure of energy without accomplishing any useful work.

Pulse-chase. An experiment in which a short labeling period is followed by the addition of an excess of the same, unlabeled compound to dilute out the labeled material. Useful for observing time-dependent behavior of compounds.

Purine. A heterocyclic ring structure with varying functional groups. The purines adenine and guanine are found in both DNA and RNA.

Puromycin. An antibiotic that inhibits polypeptide synthesis by competing with aminoacyl-tRNA for the ribosomal binding site A.

Pyranose. A simple sugar containing the six-membered pyran ring.

Pyrimidine. A heterocyclic six-membered ring structure. Cytosine and uracil are the main pyrimidines found in RNA, and cytosine and thymine are the main pyrimidines found in DNA.

Pyrophosphate. A molecule formed by two phosphates in anhydride linkage.


Quaternary structure. In a protein, the way in which the different folded subunits interact to form the multisubunit protein.


R group. Shorthand for the side chain of an amino acid.

R loop. A triple-stranded structure in which RNA displaces a DNA strand by DNA-RNA hybrid formation in a region of the DNA.

Rapid-start complex. The complex that RNA polymerase forms at the promoter site just before initiation.

Recombination. The transfer to offspring of genes not found together in either of the parents.

Redox couple. An electron donor and its corresponding oxidized form.

Redox potential (E). The relative tendency of a pair of molecules to release or accept an electron. The standard redox potential (E0) is the redox potential of a solution containing the oxidant and reductant of the couple at standard concentrations.

Regulatory enzyme. An enzyme in which the active site is subject to regulation by factors other than the enzyme substrate. The enzyme frequently contains a nonoverlapping site for binding the regulatory factor that affects the activity of the active site.

Regulatory gene. A gene whose principal product is a protein designed to regulate the synthesis of other genes.

Renaturation. The process of returning a denatured structure to its original native structure, as when two single strands of DNA are reunited to form a regular duplex, or an unfolded polypeptide chain is returned to its normal folded three-dimensional structure.

Repair synthesis. DNA synthesis following excision (cutting out) of damaged DNA.

Repetitive DNA. A DNA sequence that is present in many copies per genome.

Replica plating. A technique in which an impression of a culture is taken from a master plate and transferred to a fresh plate. The impression can be of bacterial clones or phage plaques.

Replication fork. The Y-shaped region of DNA at the site of DNA synthesis; also called a growth fork.

Replicon. A genetic element that behaves as an autonomous replicating unit. It can be a plasmid, phage, or bacterial chromosome.

Repressor. A regulatory protein that inhibits transcription from one or more genes. It can combine with an inducer (resulting in specific enzyme induction) or with an operator element (resulting in repression).

Resonance hybrid. A molecular structure that is a hybrid of two structures that differ in the locations of some of the electrons. For example, the benzene ring can be drawn in two ways, with double bonds in different positions. The actual structure of benzene is in-between these two equivalent structures.

Restriction-modification system. A pair of enzymes found in most bacteria (but not eukaryotic cells). The restriction enzyme recognizes a certain sequence in duplex DNA and makes one cut in each unmodified DNA strand at or near the recognition sequence. The modification enzyme methylates (or modifies) the same sequence, thus protecting it from the action of the restriction enzyme.

Reverse transcriptase. An enzyme that synthesizes DNA from an RNA template, using deoxyribonucleotide triphosphates.

Rho factor. A protein involved in the termination of transcription of some messenger RNAs.

Ribose. The five-carbon sugar found in RNA.

Ribosomal RNA (rRNA). The RNA parts of the ribosome.

Ribosomes. Small cellular particles made up of ribosomal RNA and protein. They are the site, together with mRNA, of protein synthesis.

RNA (ribonucleic acid). A polynucleotide in which the sugar is ribose.

RNA polymerase. An enzyme that catalyzes the formation of RNA from ribonucleotide triphosphates, using DNA as a template.

RNA splicing. The excision of a segment of RNA, followed by a rejoining of the remaining fragments.

Rolling circle replication. A mechanism for the replication of circular DNA. A nick in one strand allows the 3' end to be extended, displacing the strand with the 5' end, which is also replicated, to generate a double-stranded tail that can become larger than the unit size of the circular DNA.


S phase. The period during the cell cycle when the chromosome is replicated.

Salting in. The increase in solubility that is displayed by typical globular proteins upon the addition of small amounts of certain salts, such as ammonium sulfate.

Salting out. The decrease in protein solubility that occurs when salts such as ammonium sulfate are present at high concentrations.

Salvage pathway. A family of reactions that permits, for instance, nucleosides as well as purine and pyrimidine bases resulting from the partial breakdown of nucleic acids to be re-utilized in nucleic acid synthesis.

Satellite DNA. A DNA fraction whose base composition differs from that of the main component of DNA, as revealed by the fact that it bands at a different density in a CsCI gradient. Usually repetitive DNA or organelle DNA.

Second messenger. A diffusible small molecule, such as cAMP, that is formed at the inner surface of the plasma membrane in response to a hormonal signal.

Secondary structure. In a protein or a nucleic acid, any repetitive folded pattern that results from the interaction of the corresponding polymeric chains. In proteins, the most common are b-strands (sheets) and a-helices.

Semiconservative replication. Duplication of DNA in which the daughter duplex carries one old strand and one new strand.

Semipermeable. The characteristic of allowing only some molecules, usually smaller or uncharged ones, to pass through.

Sigma factor. A subunit of RNA polymerase that recognizes specific sites on DNA for initiation of RNA synthesis.

Signal sequence. A (usually N-terminal) sequence of a protein that directs its processing or localization within the cell.

Single-copy DNA. A region of the genome whose sequence is present only once per haploid complement.

Site-directed mutagenesis. An intentional alteration in a DNA sequence that can be genetically inherited.

Soluble protein. See globular protein.

Somatic cell. Any cell of an organism that cannot contribute its genes to a later generation.

SOS system. A set of DNA repair enzymes and regulatory proteins that regulate their synthesis so that maximum syn thesis occurs when the DNA is damaged.

Southern blotting. A method for detecting a specific DNA restriction fragment, developed by Edward Southern. DNA from a gel electrophoresis pattern is blotted onto nitrocellulose paper; then the DNA is denatured and fixed on the paper. Subsequently the pattern of specific sequences in the Southern blot can be determined by hybridization to a suitable probe and autoradiography. A Northern blot is similar, except that RNA is blotted instead onto the nitrocellulose paper.

Splicing. See RNA splicing.

Sporulation. Formation from vegetative cells of metabolically inactive cells that can resist extreme environmental conditions.

Stacking energy. The energy of interaction that favors the face-to-face packing of purine and pyrimidine base pairs.

Steady state. In enzyme-kinetic analysis, the time interval when the rate of reaction is approximately constant with time. The term is also used to describe the state of a living cell where the concentrations of many molecules are approximately constant because of a balancing between their rate of synthesis and breakdown.

Stem cell. A cell from which other cells stem or arise by differentiation.

Stereoisomers. Isomers that are nonsuperimposable mirror images of each other.

Steroids. Compounds that are derivatives of a tetracyclic structure composed of a cyclopentane ring fused to a substituted phenanthrene nucleus.

Structural domain. An element of protein tertiary structure that forms an independent folding unit.

Structural gene. A gene encoding the amino acid sequence of a polypeptide chain.

Structural protein. A protein that serves a structural function.

Substrate. A molecule that is acted upon, and chemically changed, by an enzyme.

Subunit. Individual polypeptide chains in a protein.

Supercoiled DNA. Supertwisted, covalently-closed duplex DNA.

Suppressor gene. A gene that can reverse the phenotype of a mutation in another gene.

Suppressor mutation. A mutation that restores a function lost by an initial mutation and that is located at a site different from the initial mutation.

Svedberg unit (S). The unit used to express the sedimentation constant (S = 10-l3 sec). The sedimentation constant S is proportional to the rate of sedimentation of a molecule in a given centrifugal field and is related to the size and shape of the molecule.

Synapse. The chemical connection for communication between two nerve cells or between a nerve cell and a target cell such as a muscle cell.

Synapsis. The pairing of homologous chromosomes, seen during the first meiotic prophase.


Tandem duplication. A duplication in which the repeated regions are immediately adjacent to one another.

TCA cycle. See tricarboxylic acid cycle.

Template. A polynucleotide chain that serves as a surface for the absorption of monomers of a growing polymer and thereby dictates the sequence of the monomers in the growing chain.

Termination factors. Proteins that are exclusively involved in the termination reactions of protein synthesis on the ribosome.

Terpenes. A diverse group of lipids made from isoprene precursors.

Tertiary structure. In a protein or nucleic acid, the final folded form of the polymer chain.

Tetramer. Structure resulting from the association of four subunits.

Thioester. An ester of a carboxylic acid with a thiol or mercaptan.

Thymidine. One of the four nucleosides found in DNA.

Thymine. A pyrimidine base found in DNA.

Topoisomerase. An enzyme that changes the extent of supercoiling of a DNA duplex.

Transamination. Enzymatic transfer of an amino group from an a-amino acid to an a-keto acid.

Transcription. RNA synthesis that occurs on a DNA template.

Transduction. Genetic exchange in bacteria that is mediated via phage.

Transfection. An artificial process of infecting cells with naked viral DNA.

Transfer RNA (tRNA). Any of a family of low-molecular weight RNAs that transfer amino acids from the cytoplasm to the template for protein synthesis on the ribosome.

Transferase. An enzyme that catalyzes the transfer of a molecular group from one molecule to another.

Transformation. Genetic exchange in bacteria that is mediated via purified DNA. In somatic cell genetics the term is also used to indicate the conversion of a normal cell to one that grows like a cancer cell.

Transgenic. Describing an organism that contains transfected DNA in the germ line.

Transition state. The activated state in which a molecule is best suited to undergoing a chemical reaction.

Translation. The process of reading a messenger RNA sequence for the specified amino acid sequence it contains.

Transport protein. A protein whose primary function is to transport a substance from one part of the cell to another, from one cell to another, or from one tissue to another.

Tricarboxylic acid (TCA) cycle. The cyclical process whereby acetate is completely oxidized to CO2 and water, and electrons are transferred to NAD+ and flavine. The TCA cycle is localized to the mitochondria in eukaryotic cells and to the plasma membrane in prokaryotic cells. Also called the Krebs or citric acid cycle.

Trypsin. A proteolytic enzyme that cleaves (cuts) peptide chains next to the basic amino acids arginine and Iysine.

Tryptic peptide mapping. The technique of generating a chromatographic profile characteristic of the fragments resulting from trypsin enzyme cleavage of the protein.

Tumorigenesis. The mechanism of tumor formation.

Turnover number. The maximum number of molecules of substrate that can be converted to product per active site per unit time.


Ultracentrifuge. A high-speed centrifuge that can attain speeds up to 60,000 rpm and centrifugal fields of 500,000 times gravity. Useful for characterizing and/or separating macromolecules.

Unidirectional replication. See bidirectional replication.

Unwinding proteins. Proteins that help to unwind double-stranded DNA during DNA replication.

Urea cycle. A metabolic pathway in the liver that leads to the synthesis of urea from amino groups and CO2. The function of the pathway is to convert the ammonia resulting from catabolism to a nontoxic form, which is then secreted.

UV irradiation. Electromagnetic radiation with a wavelength shorter than that of visible light (200-390 nm). Causes damage to DNA (mainly by forming pyrimidine dimers).


van der Waals forces. Refers to the combined effect of two types of interactions, one attractive and one repulsive. The attractive forces are due to favorable interactions among the induced instantaneous dipole moments that arise from fluctuations in the electron charge densities of neighboring nonbonded atoms. Repulsive forces arise when noncovalently bonded atoms come too close together.

Viroids. Pathogenic agents, mostly of plants, that consist of short (usually circular) RNA molecules.

Virus. A complex of nucleic-acid and protein, that can infect and replicate inside a specific host cell to make more virus particles.

Vitamin. A trace organic substance required in the diet of some species. Many vitamins are precursors of coenzymes.


Watson-Crick base pairs. The type of hydrogen-bonded base pairs found in DNA, or comparable base pairs found in RNA. The base pairs are A-T, G-C, and A-U.

Western blot. Similar in principle to a Southern blot, but where the species adsorbed to the nitrocellulose filter is a protein, and the detection makes use of specific antibodies.

Wild-type gene. The form of a gene (allele) normally found in nature.

Wobble. A proposed explanation for base pairing that is not of the Watson-Crick type and that often occurs between the 3' base in the codon and the 5' base in the anticodon.


X-ray crystallography. A technique for determining the structure of molecules from the X-ray diffraction patterns that are produced by crystalline arrays of the molecules.


Ylid. A compound in which adjacent, covalently-bonded atoms, both having an electronic octet, have opposite charges.


Z form. A duplex DNA structure in which there is the usual type of hydrogen bonding between the base pairs but in which the helix formed by the two polynucleotide chains is left-handed rather than right-handed.

Zwitterion. A dipolar ion with spatially-separated positive and negative charges. For example, most amino acids are zwitterions, having a positive charge on the a-amino group and a negative charge on the a-carboxyl group but no net charge on the overall molecule.

Zygote. A cell that results from the union of haploid male and female sex cells. Zygotes are diploid.

Zymogen. An inactive precursor of an enzyme. For example, trypsin exists in the inactive form trypsinogen before it is converted to its active form, trypsin.


Revised 96.11.19 by stefan@xray.bmc.uu.se